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MyHR Integrations - FAQ & Troubleshooting

This article covers common questions and issues across all MyHR payroll integrations. Where behaviour differs by payroll, we've called it out.

Contents

Overview

Employee creation failures

MyHR failed to add a new employee to payroll 

When a new employee signs their agreement in MyHR, their record is automatically created in your payroll system (if you have that setting enabled). If it fails, you'll receive an email and the person will appear as Action required in your integration.

Two main causes:

  1. Integration settings — something required by your payroll system isn't configured in MyHR (most commonly a User-Defined Group or Cost Centre default for iPayroll and CloudPayroll)
  2. Employee details — the person's data is failing validation in payroll (e.g. invalid bank account number, missing date of birth)

To fix it:

  1. Go to Settings > Settings > Integrations, find your payroll and select Manage
  2. In the Manage tab, filter by Action required
  3. Select the ellipsis (...) next to the person and choose View profile — the error will be listed
  4. Fix the issue:
    • Settings error (User-Defined Groups, Cost Centres): go to the Settings tab in your integration and set a default value
    • Person details error: open their MyHR profile and correct the information
  5. Back in the Manage tab, find the person and select Save and sync
  6. Their status should change to Connected within a few minutes

If the error won't clear, you can create the employee directly in payroll and then link them back to MyHR:

  1. In the Manage tab, select the ellipsis (...) next to the person
  2. Choose Create a new payroll profile
  3. Use the Refresh button to pull the latest data, then link the profiles manually

CloudPayroll specific: Date of birth is a required field for CloudPayroll. If it's missing from the employee's profile in MyHR, the creation will fail.

iPayroll specific: If User-Defined Groups or Cost Centres are mandatory in your iPayroll account, you must set a default value in your MyHR integration settings — otherwise every new employee will fail.


Leave sync failures 

MyHR failed to send leave to payroll 

When leave is approved in MyHR, it's sent to your payroll system automatically. If it fails, MyHR retries up to five times. If all five attempts fail, the payroll administrator receives an email explaining why.

At that point MyHR stops retrying — the payroll administrator needs to enter the leave manually in payroll.

Common reasons leave fails to send:

  • Leave starts or ends on a public holiday (most payroll systems won't accept this — see below)
  • Too many hours requested on a day relative to the employee's work schedule
  • The employee's ID was changed in payroll, breaking the link to MyHR
  • Leave falls in an open pay run (it can no longer be modified)

Why can't annual leave start or finish on a public holiday?

Public holidays are paid separately — they can't be taken as annual leave. Most payroll systems will reject a leave request that starts or ends on one.

The fix: cancel the leave and re-request it with dates that avoid the public holiday. If the employee genuinely needs to record something across that period, shift the start or end date by one day and request 0 hours on the extra day.

Leave is in an open pay run and can't be cancelled

Once leave enters an open pay run in payroll, it's locked. Neither MyHR nor the employee can cancel it from either side. The payroll administrator needs to handle it directly in the payroll system.

 Leave balances look wrong

Why is the balance in MyHR different to what payroll shows?

MyHR and payroll systems display leave balances differently — both numbers are correct, they're just showing different things. The table below explains what MyHR shows for each payroll:

Payroll What payroll shows What MyHR shows
iPayroll Balance at last pay run Balance at last pay run minus approved leave not yet paid out
CloudPayroll Live balance (includes accruals in open pay runs) Live balance minus approved leave not yet paid out
PayHero Entitlement plus estimated accrued Entitlement plus estimated accrued (same — but see note below)
Xero NZ / AU Leave balances not synced Leave request status only — no balance shown
MyHR Payroll AU Live balance Live balance minus approved leave not yet paid out

PayHero specific: PayHero doesn't tell MyHR about approved-but-unpaid leave. This means the balance shown in MyHR does not decrease when leave is approved — it only updates once the employee has been paid. This is a known API limitation, not a bug.

Xero specific: Leave balances do not sync for Xero NZ or Xero AU. Employees will not see leave balance wheels in MyHR when connected to Xero — only leave request status is shown.

To force a balance refresh: go to the person's Leave tab in their MyHR profile. The Overview tab does not trigger a refresh.

Employee can't see their leave balances

Work through these checks in order:

  1. Are they linked? Go to Settings > Settings > Integrations > [your payroll] > Manage. Find the person and confirm their status is Connected. If not, see the linking instructions in your payroll's integration article.
  2. Do they have balances in payroll? Log in to your payroll system and check the employee's leave balances there. If they're empty in payroll, they'll be empty in MyHR too. New employees may not have balances until they've been through a pay run.
  3. Are the balance types set to visible? Go to the Settings tab in your integration and check that the relevant leave balance types are toggled on for management or self-service.
  4. Has their payroll ID changed? If someone changes an employee's ID in the payroll system, MyHR loses the link silently. See Broken employee link below.

Broken employee link

An employee's payroll ID was changed — now the link is broken

If an employee's ID is changed in the payroll system, MyHR can no longer match the records. It imports the person as a new, unlinked payroll profile — the old linked profile becomes a ghost record.

Signs of a broken link: employee suddenly can't see leave balances, status changes from Connected to Not linked, or a duplicate payroll profile appears in the Manage tab.

To fix it:

  1. Go to Settings > Settings > Integrations > [your payroll] > Manage
  2. Find the person and select the ellipsis (...) > Unlink to disconnect from the old record
  3. Find the old/ghost payroll record and select Exclude from payroll so it stops appearing
  4. Find the person again and select Link to an existing payroll profile to connect them to the correct (new) record

Leave types and visibility

What leave types can employees request?

For employees linked to a payroll system, available leave types are pulled directly from payroll — only types configured as available for leave requests in your payroll will appear in MyHR.

For employees not linked to payroll, the default types are: Annual Leave, Sick Leave, Bereavement Leave, Domestic Violence Leave, Alternative Leave, and Unpaid Leave.

PayHero specific: Leave in PayHero is requested in days (not hours, unlike iPayroll and CloudPayroll). Full day, or fractions (0.75, 0.5, 0.25) for single-day requests. Multi-day requests must be whole days.

iPayroll specific: Parental leave is not available via the iPayroll API — it must be set up directly in iPayroll by the payroll administrator.

How to change which leave balances are visible in MyHR

  1. Go to Settings > Settings > Integrations
  2. Find your payroll and select Manage
  3. Select the Settings tab
  4. In the leave balance section, set visibility for management and self-service employees
  5. Select Save

You can show different balances to managers versus employees — for example, hiding sick leave balances from self-service while keeping them visible to managers.

Will custom leave types from payroll show in MyHR?

Yes — custom leave balances sync from payroll overnight, or immediately when someone visits the Leave area in MyHR. Once synced, configure their visibility in your integration settings as above.

For iPayroll: custom leave types show as Payments Special Leave in iPayroll. Only types with Available for Leave Request checked will appear in MyHR. You can manage this under iPayroll Setup > Pay Elements > Leave > Payments Only.

Pay rates

Do pay rates sync to payroll automatically?

Yes — pay rates are included in the automatic data push for all supported payroll integrations. This covers both new employee creation and ongoing updates (e.g. after a pay review).

To enable this, turn on Push Updates in your integration settings. See Automatic data updates between MyHR and payrolls for setup instructions.

iPayroll specific: You'll need to re-authorise your iPayroll connection before pay rates will be included in automatic pushes. See Re-authorising your integration to iPayroll.

Important: Only the first/main pay rate is updated via automatic push. If an employee has multiple pay rates in payroll, additional rates need to be managed directly in the payroll system.

Automatic data updates

What employee details get pushed to payroll automatically?

See the full list and setup guide at Automatic data updates between MyHR and payrolls.

Known limitations across payrolls:

  • Hours of work — standalone changes to hours may not push on some payrolls (CloudPayroll, Xero AU). If employment type changes from part-time to full-time in CloudPayroll, hours may be cleared — check and update in payroll.
  • Fixed-term employment type (Xero NZ and AU) — changes to fixed-term won't push automatically. Update directly in Xero.
  • Weekly wage employees (iPayroll) — not supported for automatic data push. Manage directly in iPayroll.
  • Email address — coming soon for all payrolls.
  • Multiple pay rates — only the first/main rate is updated automatically.

Lost authentication / re-authorisation

My integration has failed authentication

You'll see a Failed auth status in your integrations list and a reminder banner in MyHR. This usually happens when payroll credentials expire or are changed.

While authentication is in a failed state, employee data and leave won't sync. Once re-authorised, contact us via the Ask Us chat if you need any changes that were missed during the outage to be sent across.

Other common issues

A duplicate payroll profile has appeared in the Manage tab

This usually means an employee's ID was changed in payroll. MyHR imported the new profile as an unlinked record. See Broken employee link above.

Leave approved for a previous pay period — will it still send?

Yes — leave can be sent to payroll after a pay period has closed, as long as it's not in an open pay run. Once it's in an open pay run it's locked and must be handled directly in payroll.

 

An employee was added to payroll directly (not through MyHR) — do I need to do anything?

Yes — you'll need to link them manually. Go to Settings > Settings > Integrations > [your payroll] > Manage and link the payroll profile to their MyHR profile. See Navigating integrations in MyHR for full linking instructions.

Support Options

If you need more help, our HR teams are always here for you!

If you have questions, message the MyHR team via the Ask Us chat feature or call us on:
NZ - 0800 69 47 69 (0800 MY HR NZ) or +64 9 887 3345
AU - 02 7908 2240